Securing a single folder locking down all other services?

We've ran into this a few times now and it's both confusing and frustrating. All of our services are unsecured by default. However, I created an "Internal" folder and secured it. Following that, all of the unsecured services were acting like they were secured as well (i.e. prompting for a login).

We have a flex app that consumes those unsecured services and it was throwing errors indicating that it wasn't able to reach the services because they were secured (although they weren't). After I unsecured the secured folder, the flex app worked just fine.

Why would securing a folder with no services in it have any effect on other services? Any help would be very much appreciated!

Are you using GIS Server Tier or Web Tier authentication? We use Web Tier and at 10.1 if you secure using that, the whole server is secured. I think with GIS Server Tier you can pick and choose which services and folders to secure.

At 10.2 you can have secured and unsecured services using Web Tier and multiple Web Adaptors but not at 10.1.